SIGNAL-seq: Multimodal Single-cell Inter- and Intra-cellular Signalling Analysis II

We present SIGNAL-seq (Split-pool Indexing siGNalling AnaLysis by sequencing): a multiplexed split-pool combinatorial barcoding method that simultaneously measures RNA and post-translational modifications (PTMs) in fixed single cells from 3D solid-tumour models. SIGNAL-seq PTM measurements are equivalent to mass cytometry and RNA gene detection is analogous to split-pool barcoding scRNA-seq. By measuring both mRNA ligand-receptor pairs and PTMs in single cells, SIGNAL-seq simultaneously reveals both inter- and intra-cellular signalling in tumour microenvironment organoids. SIGNAL-seq was performed on CRC patient derived organoids (PDOs) +/- CAFs in 3D, and treated +/- SN-38 chemotherapy. This patient-derived 3D model system provides a dynamic range of cell-fates driven by both inter-cellular communication and chemotherapy. Further information on the SIGNAL-seq barcoding layout and processed data can be found at: https://github.com/TAPE-Lab/SIGNAL-seq